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Jean-Christophe Lagier,1,2 Matthieu Million,1,2 Sébastien Cortaredona,1,3 Léa Delorme,1 Philippe Colson,1,2 Pierre-Edouard Fournier,1,3 Philippe Brouqui,1,2 Didier Raoult,1,2 Philippe Parola1,3 On behalf of the IHU Task Force1IHU-Méditerranée Infection, Marseille, France; 2MEPHI, Aix Marseille Université, Institut de Recherche pour le Développement, Assistance Publique Hôpitaux de Marseille, Marseille, France; 3VITROME, Aix Marseille Université, Institut de Recherche pour le Développement, Assistance Publique Hôpitaux de Marseille, Service de Santé des Armées, Marseille, FranceCorrespondence: Philippe Parola, Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, Marseille, 13005, France, Tel + 33 0 4 13 73 24 01, Fax + 33 0 4 13 73 24 02, Email philippe.parola@univ-amu.fr Jean-Christophe Lagier, Email jeanchristophe.lagier@ap-hm.frObjectives: We evaluated the 6-week mortality of SARS-CoV-2 hospitalized patients treated using a standardized protocol in 2020 in Marseille, France.Methods: A retrospective monocentric cohort study was conducted in the standard hospital wards at the Institut Hospitalo-Universitaire Méditerranée Infection, between March and December 2020 in adults with SARS-CoV-2 PCR-proven infection.Results: Of the 2111 hospitalized patients (median age, 67 [IQR 55– 79] years; 1154 [54.7%] men), 271 were transferred to the intensive care unit (12.8%) and 239 died (11.3%; the mean age of patients who died was 81.2 (± 9.9)). Treatment with hydroxychloroquine plus azithromycin (HCQ-AZ), used in 1270 patients, was an independent protective factor against death (0.68 [0.52 – 0.88]). This effect was consistent for all subgroups of age, comorbidities, severity of the disease and comedications with zinc or corticosteroids. Zinc was independently protective against death (0.39 [0.23 – 0.67]), in a subgroup analysis of patients treated with HCQ-AZ without dexamethasone. The use of high-flow oxygen therapy in elderly patients who were not eligible for intensive care unit transfer saved 19 patients (33.9%).Conclusions: In our 2020 cohort, treating COVID-19 with HCQ-AZ was associated with lower mortality. These results need to be analyzed in the context of academic discussions about observational studies versus randomized clinical trials. More data will deserve to be analyzed in the SARS-Cov 2 variants, vaccination and post-vaccination era.Keywords: SARS-CoV-2, COVID-19, hydroxychloroquine, azithromycin

Background: The genus Bartonella is composed of Gram-negative, fastidious, facultative intracellular bacteria that can cause bacteremia in mammals and various disorders in humans. Rodents have been reported as reservoirs of more than 30 Bartonella species, seven of which cause zoonotic infections. Materials and Methods: In the present study, the isolation of Bartonella sp. was attempted from 150 spleen samples from 13 rodent species (mostly Apodemus species) from three geographically different regions in Turkey. Results: Bartonella sp. was successfully isolated from 65 of these 150 samples (43%). The prevalences of Bartonella sp. in tested rodents in the regions of Giresun, Yozgat, and Burdur were 68%, 44%, and 16%, respectively. Using polymerase chain reaction/sequence analysis of the citrate synthase-coding gene ( gltA ), Bartonellaisolates were classified seven species including B. taylorii , B. grahamii , B. birtlesii , B. mastomydis , and three putatively new Bartonella species. We performed further identification techniques for one of the three Bartonella species that were different from the validated Bartonella species according to the gltA sequence analysis. Conclusion: Here, we report the genomic and phenotypic characterization of Bartonella sp. strain G70 that was isolated from the splenic tissue of an Apodemus uralensis (Pallas 1881), the Ural field mouse, captured in the Giresun region of northeastern Turkey. Bartonella sp. strainG70 (RSKK 22001) was characterized by whole genome and partial gene ( gltA , 16S ribosomal RNA) sequencing and comparison, scanning electron microscopy, biochemical tests, and matrix-assisted laser desorption ionization time-of-flight mass spectrometry. This novel Bartonella is a Gram-negative, rod-shaped bacterium and has neither flagella nor pili. The genome from strain G70 was 1,606,969-bp-long with a G + C content of 35.7%. Bartonella rochalimae was found to be the closest phylogenetic relative of strain G70 (OrthoANI = 90.5%, digital DNA-DNA hybridization = 41.4%). We therefore propose that this new species be named Bartonella bilalgolemii sp. nov. with strain G70 T as the type strain.

One of the main barriers for the implementation of metagenomic sequencing in routine diagnosis of infectious diseases is the presence of host DNA. While several enrichment methods are likely to overcome this issue, their effectiveness for specimens such as bone in the case of chronic infections remains to be determined. We compared the relevance of two methods for bacterial DNA enrichment when compared to a reference protocol during pretreatment of bone samples from fracture-related infections before HTS by both Illumina Miseq and Oxford Nanopore Technology (ONT). The bacterial/human DNA ratio was higher for either protocols than the reference technique (p = 0.00012), without any significant difference between them. HTS sensitivity over culture ranged from 21.7 % to 85 %. The ability of the studied protocols to improve the bacterial/human DNA ratio depends on the sequencing technique employed. In this context, there is room for improvement in enhancing the sensitivity of HTS for diagnostic purpose., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: David DELARBRE reports administrative support was provided by Hôpital Sainte Musse. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

The aim of this study was to assess the prevalence of Coxiella burnetii infection among veterinary medicine students from two Bulgarian Universities, located in Sofia and Stara Zagora. Blood samples were collected from a total of 185 veterinary students for the detection of C. burnetii phase II antibodies and presence of DNA using an enzyme-linked immunosorbent assay (ELISA) and end-point PCR test. Out of all samples, 29.7% were positive for at least one C. burnetii phase II antibody marker or by the result of the PCR test. Veterinary students from Stara Zagora showed a significantly high seropositivity for Q fever (33.6%), as compared to the students in Sofia (23%; p < 0.05). Evidence of recent exposure with detection of anti- C. burnetii phase II IgM (+) antibodies was observed in 14.6% of the students under study. Seroprevalence among students in Stara Zagora was higher (15.3%). Anti- C. burnetii phase II IgG antibodies were detected in 21.6% of examined samples. Our study revealed a higher seropositivity among the male students (32.8%) as compared to females (16.0%; p < 0.05). The end-point PCR assay detected 5.9% blood samples as positive. The relative risk (RR) of Q fever exposure for male students was 40.7%, whereas it was 24.6% in females ( p < 0.05). The findings from this study indicate that the C. burnetii infection is widely distributed amongst veterinary students in Bulgaria. This study emphasizes the need for improved safety protocols and infection control measures in veterinary training programs.

We report a large-scale outbreak of Mycoplasma pneumoniae respiratory infections encompassing 218 cases (0.8% of 26,449 patients tested) during 2023-2024 in Marseille, France. The bacterium is currently circulating and primarily affects children <15 years of age. High prevalence of co-infections warrants the use of a syndromic diagnostic strategy.

Objectives: This study aimed to investigate the prevalence of mpox virus (MPXV) infections in the general population consulting for routine sexually transmitted infections (STIs) in our Marseille public hospital. In fact, the recent worldwide MPXV outbreak mainly impacted men who have sex with men and the prevalence of MPXV infections in the general population remains poorly defined., Methods: All samples addressed routinely to our microbiological laboratory for STIs between July 1 and October 15, 2022 were screened with MPXV-specific quantitative polymerase chain reaction., Results: A total of 2688 samples from 1896 patients suspected of having STIs were tested and eight (0.4%) patients were incidentally diagnosed with MPXV infection, including six men and two women. MPXV was detected in rectal swabs (n = 2), urine (n = 2), vaginal swabs (n = 2), a urethral swab (n = 1), and a skin swab (n = 1)., Conclusions: This study suggests that some MPXV infections are likely to be underdiagnosed because of their non-specific clinical presentation and/or insufficient clinical knowledge of the disease. Our data showed that systematic screening was particularly useful for detecting MPXV in patients without classic lesions or cases of asymptomatic carriage in patients reporting recent high-risk exposure and in patients presenting no obvious risk factor., Competing Interests: Declarations of competing interests The authors have no competing interests to declare., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

The rapid genetic evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the coronavirus disease 2019 (COVID-19) pandemic has greatly challenged public health authorities worldwide, including in Mauritania. Despite the presence of the virus in Mauritania, only one study described its genomic variation during the course of the epidemic. The purpose of the present study was to document the genomic pattern of SARS-CoV-2 variants from clinical isolates during the COVID-19 outbreak in Mauritania, from September to November 2021. The whole genomes from 54 SARS-CoV-2 strains detected in nasopharyngeal swabs with a cycle threshold value ≤ 30 were successfully sequenced using next-generation sequencing (NGS) and the Illumina protocol. The mean genome coverage (±standard deviation) was 96.8% (±3.7). The most commonly identified clade was 21J (57.4%), followed by 21D (16.7%), 20A (11.1%), and 20B (9.2%). At the level of lineages, the majority of the samples were Delta variants with the sub-lineage AY.34 (or B.1.617.2.34). Among the 54 SARS-CoV-2 isolates that were successfully sequenced, 33 (61.1%) came from vaccinated individuals, and 21 (38.9%) were from unvaccinated individuals. Several SARS-CoV-2 variants were present in Mauritania between September and November 2021. As Mauritania, like many West African countries, is resource-limited regarding viral genome sequencing facilities, establishment of mutualized sub-regional sequencing platforms will be necessary to ensure continuous monitoring of mutations in viral genomes and track potential reduction in COVID-19 vaccine efficacy, increased transmissibility, and disease severity.

We report a case of exposure to Coxiella burnetii in a surgical nurse who underwent an injury of her finger with a scalpel blade during a native aortic valve replacement with a bio-prosthetic cardiac valve conducted on a patient suffering from C. burnetii aortic endocarditis. Given the positivity of C. burnetii culture and PCR from the patient's aortic valve, she was prescribed prophylactic doxycycline 100 mg twice a day for 10 days. Q fever is an occupational zoonosis resulting usually of exposure to infected animals by inhalation of infected aerosols or consumption of contaminated raw milk. Apart from materno-foetal transmission, about 180 cases of human-to-human C. burnetii transmission have been published from 1949 to today, including transmission by blood transfusion, sexual relations, transmission in the healthcare setting to staff, patient attendants and other patients that were likely infected from inhalation of aerosol from respiratory or placental products, transmission to staff during autopsies of patients with Q fever and transmission in familial settings. As C. burnetii is a highly infectious bacterium, that may cause infection with a low inoculum, it should be added to the list of organisms which may be of concern following blood exposure among healthcare professionals.

Aiming at identifying the reservoir and contamination sources of Coxiella burnetii in Northern Algeria, we investigated the molecular presence of the bacterium in 599 samples (blood, placenta, liver, spleen, and uterus) collected from cattle, sheep, dogs and cats. Our qPCR results showed that 15/344 (4.36%) blood samples and six/255 (2.35%) organ specimens were positive for C. burnetii. In cattle, three (4%) blood and liver samples were positive. In sheep, one blood (1.19%) and 3 (8.57%) placenta samples were positive. At the Algiers dog pound, 8 (10%) and 3 (5%) blood samples were qPCR positivein dogs and cats, respectively. In addition, MST genotyping showed that MST 33 was present in cattle and sheep, MST 20 in cattle,andMST 21 in dogs and cats., Competing Interests: Declaration of Competing Interest The authors declare that there are no conflicts of interest., (Copyright © 2024. Published by Elsevier Ltd.)

Opinion 129 addresses the status of Firmicutes corrig. Gibbons and Murray 1978 (Approved Lists 1980). The name has the category 'division' and was included in the Approved Lists of Bacterial Names, although that category had previously been removed from the International Code of Nomenclature of Bacteria (1975 revision onwards). When the category 'phylum' was introduced into the International Code of Nomenclature of Prokaryotes (ICNP) in 2021, equivalence between 'phylum' and 'division' was not stipulated. Since the definition of the taxonomic categories and their relative order is one of the principal tasks of every code of nomenclature, the inclusion of Firmicutes corrig. Gibbons and Murray 1978 in the Approved Lists was an error. The name is either not validly published or illegitimate because its category is not covered by the ICNP. If Firmicutes corrig. Gibbons and Murray 1978 (Approved Lists 1980) was a validly published phylum name, it would be illegitimate because it would contravene Rule 8, which does not permit any deviation from the requirement to derive a phylum name from the name of the type genus. Since Firmicutes corrig. Gibbons and Murray 1978 is also part of a 'misfitting megaclassification' recognized in Opinion 128, the name is rejected, without any pre-emption regarding a hypothetically validly published name Firmicutes at the rank of phylum. Gracilicutes Gibbons and Murray 1978 (Approved Lists 1980) and Anoxyphotobacteriae Gibbons and Murray 1978 (Approved Lists 1980) are also rejected. The validly published phylum names have a variety of advantages over their not validly published counterparts and cannot be replaced with ad hoc names suggested in the literature. To ease the transition, it is recommended to mention the not validly published phylum names which strongly deviate in spelling from their validly published counterparts along with the latter in publications during the next years.

Bartonella quintana is a louse-borne gram-negative bacillus that remains a poorly characterized cause of bacteremia, fever, and infective endocarditis. Due to the link with pediculosis, B quintana transmission is tied to poverty, conflict, overcrowding, and inadequate water access to maintain personal hygiene. Although these risk factors may be present globally, we argue that a substantial burden of undocumented B quintana infection occurs in Africa due to the high prevalence of these risk factors. Here, we describe the neglected burden of B quintana infection, endocarditis, and vector positivity in Africa and evaluate whether B quintana meets criteria to be considered a neglected tropical disease according to the World Health Organization., Competing Interests: Potential conflicts of interest. All authors: No reported conflicts., (© The Author(s) 2023. Published by Oxford University Press on behalf of Infectious Diseases Society of America.)

Rickettsia helvetica has been reported at varying prevalences in Danish and other European Ixodes ricinus populations. Though apparently widespread and with reported cases of human infection, the significance of the bacteria as a threat to public health remains unclear. We present a nation-wide survey of rickettsia in ticks, roe deer and humans in Denmark. Ticks were collected by flagging and screened for presence of rickettsial DNA by polymerase chain reaction. Sera from roe deer, hunters, neuroborreliosis patients and blood donors were analyzed for presence of anti-R. helvetica and Rickettsia felis antibodies by immunofluorescence microscopy. The Rickettsia minimum infection rate in ticks was 4.9 % (367/973 pools positive, 7510 ticks in total), with 3.9 % in nymphs and 9.3 % in adults. Rickettsia helvetica accounted for 4.17 % and Rickettsia monacensis for 0.03 %, 0.6 % comprised non-differentiable rickettsial DNA. The prevalence of antibodies against R. helvetica was 2.8 % (9/319) in roe deer, while no hunters (n = 536) or blood donors (n = 181) were positive. The prevalence of anti-R. helvetica antibodies among Lyme neuroborreliosis patients was 6 % (3/47), where it co-occurred with Anaplasma phagocytophilum. Based on our study autochthonous rickettsiosis is of limited concern to the public health in Denmark, but our finding of R. monacensis for the first time in Denmark illustrates the dynamic nature of tick-borne pathogens, emphasizing that continuous surveillance is necessary., Competing Interests: Declaration of Competing Interest The authors declare no conflicts of interest., (Copyright © 2023. Published by Elsevier GmbH.)

Background: Bartonella spp. are fastidious bacteria frequently identified as the cause of blood culture-negative (BCN) endocarditis. However, Bartonella infections are difficult to diagnose in routine laboratory testing and their incidence is probably underestimated. We investigated the epidemiological and clinical features of Bartonella endocarditis cases diagnosed between 2009 and 2021 on Reunion Island (Southwest Indian Ocean)., Method: We retrospectively included all patients diagnosed with Bartonella endocarditis at Reunion Island University Hospital during this period. Endocarditis was diagnosed on the basis of microbiological findings, including serological tests (IFA) and PCR on cardiac valves, and the modified Duke criteria. We used then the multispacer typing (MST) method to genotype the available Bartonella strains., Findings: We report 12 cases of B. quintana endocarditis on Reunion Island (83.3% in men, median patient age: 32 years). All the patients originated from the Comoros archipelago. The traditional risk factors for B. quintana infection (homelessness, alcoholism, exposure to body lice) were absent in all but two of the patients, who reported head louse infestations in childhood. Previous heart disease leading to valve dysfunction was recorded in 50% of patients. All patients underwent cardiac valve surgery and antimicrobial therapy with a regimen including doxycycline. All patients presented high C-reactive protein concentrations, anemia and negative blood cultures. The titer of IgG antibodies against Bartonella sp. exceeded 1:800 in 42% of patients. Specific PCR on cardiac valves confirmed the diagnosis of B. quintana endocarditis in all patients. Genotyping by the MST method was performed on four strains detected in preserved excised valves and was contributive for three, which displayed the MST6 genotype., Conclusions: Bartonella quintana is an important cause of infective endocarditis in the Comoros archipelago and should be suspected in patients with mitral valve dysfunction and BCN from this area., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Sarsiat et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

West Africa faced the COVID-19 pandemic in early March 2020 and, as of March 31, 2022, had more than 900,000 confirmed cases and more than 12,000 deaths. During this period, SARS-CoV-2 genomes evolved genetically, resulting in the emergence of distinct lineages. This review was conducted to provide the epidemiological profile of COVID-19, the mutational profile of SARS-CoV-2, and the dynamics of its lineages in the 16 west African countries by analyzing data from 33 studies and seven situation reports. For a more complete representation of the epidemiology and genetic diversity of SARS-CoV-2, we used reliable public data in addition to eligible studies. As of March 31, 2022, the 16 west African countries experienced four epidemic waves with variable intensities. Higher mortality was noted during the third wave with a case fatality rate (CFR) of 1.9%. After these four epidemic waves, Liberia recorded the highest CFR (4.0%), whereas Benin had the lowest CFR (0.6%). Through mutational analysis, a high genetic heterogeneity of the genomes was observed, with a predominance of mutations in the spike protein. From this high mutational rate, different lineages emerged. Our analysis of the evolutionary diversity allowed us to count 205 lineages circulating in west Africa. This study has provided a good representation of the mutational profile and the prevalence of SARS CoV-2 lineages beyond the knowledge of the global epidemiology of the 16 African countries.

Blood is a precious biological liquid that is normally sterile. Therefore, bacteria in the bloodstream are shown a priori anomaly. A blood culture is systematically performed to diagnose the cause of the bacteremia. Indeed, a patient received in our service had a thalassemia major and underwent a genoidentical transplant. Then, a blood test was performed to diagnose a four-day fever. In this context, we have isolated strain Marseille-Q2617 from the blood sample. It revealed a new bacterial strain that belongs to the genus Streptococcus. It is a Gram-positive coccus, nonmotile, and nonspore forming. The major fatty acid found is hexadecanoic acid, with 49.5%. A taxonomic method was used to characterize the strain by studying their phenotypic, phylogenetic, and genomic characteristics. In addition, sequence analysis of the 16S rRNA gene shows that the strain Marseille-Q2617 has 99.94% sequence similarity to Streptococcus mitis . Average nucleotide identity (ANI) analysis for strain Marseille-Q2617 T showed the highest similarity of 92.9% with S. mitis . The DNA-DNA hybridization value obtained (50.2%) between strain Marseille-Q2607 and S. mitis , its closest related species, was below the recommended threshold (<70%). Strain Marseille-Q2617 T has a genome size of 2.02 Mbp with 40.5 mol% of G + C content. Based on these results, we propose a new species of the genus Streptococcus , for which the name Streptococcus thalassemiae sp. nov., Marseille-Q2617 T (=CSUR Q2617 = CECT 30109) was proposed., Competing Interests: The authors declare that they have no conflicts of interest., (Copyright © 2023 Fatou Samba Diouf et al.)

The novel bacterial strain Marseille-P4005 T was isolated from the stool sample of a healthy donor. It is a Gram-stain negative, non-motile, non-spore-forming rod. It grew optimally at 37 °C and at pH 7.0 on 5% sheep blood-enriched Columbia agar after preincubation in a blood-culture bottle supplemented with rumen and blood. This strain does not ferment monosaccharides (except D-tagatose), disaccharides, or polymeric carbohydrates. The major cellular fatty acids were hexadecenoic (24.6%), octadecanoic (22.8%), and tetradecanoic (20.1%) acids. Next-generation sequencing revealed a genome size of 3.2 Mbp with a 56.4 mol% G + C. Phylogenetic analysis based on the 16S rRNA gene highlighted Agathobaculum desmolans strain ATCC 43058 T as the closest related strain. The OrthoANI, AAI, and digital DNA-DNA hybridization values were below the critical thresholds of 95%, 95-96%, and 70%, respectively, to define a novel bacterial species. Antibiotic resistance genes APH(3')-IIIa, erm(B), and tet(W) were detected with high identity percentages of 100%, 98.78%, and 97.18% for each gene, respectively. The APH(3')-IIIa gene confers resistance to amikacin, erm(B) gene confers resistance to erythromycin, lincomycin, and clindamycin, while tet(W) gene confers resistance to doxycycline and tetracycline. Based on KEGG BlastKOALA analyses, the annotation results showed that our strain could use glucose to produce L-lactate and pyruvate but not acetate or ethanol. Also, strain Marseille-P4005 T was predicted to use phenylalanine to produce indole, a major intercellular signal molecule within the gut microbial ecosystem. Through having a gene coding for tryptophan synthase beta chain (trpB), strain Marseille-P4005 T could produce L-tryptophan (an essential amino acid) from indole. Strain Marseille-P4005 T showed its highest prevalence in the human gut (34.19%), followed by the reproductive system (17.98%), according to a query carried out on the Integrated Microbial NGS (IMNGS) platform. Based on phylogenetic, phenotypic, and genomic analyses, we classify strain Marseille-P4005 T (= CSUR P4005 = CECT 9669), a novel species within the genus Agathobaculum, for which the name of Agathobaculum massiliense sp. nov. is proposed., (© 2023. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)

Two new bacterial strains, Marseille-P2698 T (CSUR P2698 = DSM 103,121) and Marseille-P2260 T (CSUR P2260 = DSM 101,844 = SN18), were isolated from human stools by the culturomic method. We used the taxonogenomic approach to fully describe these two new bacterial strains. The Marseille-P2698 T strain was a Gram-negative, motile, non-spore-forming, rod-shaped bacterium. The Marseille-P2260 T strain was a Gram-positive, motile, spore-forming rod-shaped bacterium. Major fatty acids found in Marseille-P2698 T were C 15:0 iso (63%), C 15:0 anteiso (11%), and C 17:0 3-OH iso (8%). Those found in Marseille-P2260 T strain were C 16:00 (39%), C 18:1n9 (16%) and C 18:1n7 (14%). Strains Marseille-P2698 T and Marseille-P2260 T had 16S rRNA gene sequence similarities of 91.50% with Odoribacter laneus T , and of 90.98% and 95.07% with Odoribacter splanchnicus T and Eubacterium sulci T , respectively. The exhibited digital DNA-DNA Hybridization values lower than 20.7%, and Orthologous Average Nucleotide Identity values lower than 73% compared to their closest related bacterial species O. splanchnicus T and E. sulci T respectively. Phenotypic, biochemical, phylogenetic, and genomic results obtained by comparative analyses provided sufficient evidence that both of the two studied strains Marseille-P2698 T and Marseille-P2260 T are two new bacterial species and new bacterial genera for which the names Culturomica massiliensis gen. nov., sp. nov., and Emergencia timonensis gen. nov., sp. nov. were proposed, respectively., (© 2023. The Author(s).)

We used whole genome sequencing to identify and analyze mutations in SARS-CoV-2 in urban settings during the deadliest wave of the COVID-19 epidemic-from March to April 2021-in Senegal. Nasopharyngeal samples testing positive for SARS-CoV-2 were sequenced on the Illumina NovaSeq 6000 sequencing system using the COVIDSeq protocol. A total of 291 genotypable consensus genome sequences were obtained. Phylogenetic analyses grouped the genomes into 16 distinct PANGOLIN lineages. The major lineage was B.1.1.420, despite circulation of the Alpha variant of concern (VOC). A total of 1125 different SNPs, identified relative to the Wuhan reference genome, were detected. These included 13 SNPs in non-coding regions. An average density of 37.2 SNPs per 1000 nucleotides was found, with the highest density occurring in ORF10. This analysis allowed, for the first time, the detection of a Senegalese SARS-CoV-2 strain belonging to the P.1.14 (GR/20J, Gamma V3) sublineage of the Brazilian P.1 lineage (or Gamma VOC). Overall, our results highlight substantial SARS-CoV-2 diversification in Senegal during the study period.

Bacterial strain Marseille-P3954 was isolated from a stool sample of a 35-year-old male patient living in France. It was a gram-positive, rod-shaped anaerobic, non-motile, and non-spore-forming bacterium. C 16:0 and C 18:1n9 were the major fatty acid, while its genome measured 2,422,126 bp with 60.8 mol% of G+C content. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain Marseille-P3954 had 85.51% of similarity with Christensenella minuta, its closest related species with standing in nomenclature. As this value is very low compared to the recommended threshold, it suggested that the Marseille-P3954 strain belongs to a new bacterial genus, classified in a new family. On the basis of these genomic, phenotypic, and phylogenetic evidences, we propose that strain Marseille-P3954 should be classified as a new genus and species, Maliibacterium massiliense gen. nov., sp. nov. The type strain of M. massiliense sp. nov. is Marseille-P3954 (CSUR P3954 = CECT 9568)., (© 2023. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Borrelia miyamotoi is a tick-borne zoonotic agent that causes hard tick-borne relapsing fever, an emerging disease in humans. Some small mammalian and bird species are reported to be reservoirs of B. miyamotoi. This study aims to examine Borrelia species present in rodents captured from rural areas of Turkey. Blood samples of rodents were initially screened with Borrelia 16S rRNA qPCR. The Borrelia flaB gene was subsequently amplified by conventional PCR, after which all positive samples were sequenced. Borrelia miyamotoi was observed in nine out of 536 blood samples (1.7%) collected from wild rodents. Phylogenetic analysis showed that all positive samples belonged to the European genotype clade of B. miyamotoi. PCR positivity was 5.3%, 3.7%, and 1.8% in Apodemus uralensis, Apodemus flavicollis, and Myodes glareolus, respectively. Borrelia burgdorferi sensu lato that causes Lyme borreliosis in humans could not be detected in the rodents. In this study, presence of B. miyamotoi DNA is reported for the first time in rodents in Turkey., (Copyright © 2023. Published by Elsevier GmbH.)

In Senegal, Coxiella burnetii, which causes Q fever, has often been identified in ticks and humans near livestock, which are considered to be reservoirs and main sources of infection. We describe the emergence of C. burnetii in rodents, not previously known to carry this pathogen, and describe 2 new genotypes.

Here, we reported two draft genomes of Fusobacterium simiae: strain DSM 19848, initially isolated from monkey dental plaque, and its close relative strain Marseille-Q7035, cultivated from a human intra-abdominal abscess puncture fluid. Their genome sizes are 2.4 Mb and 2.5Mb, respectively. Their G+C contents were 27.1% and 27.2%, respectively.

Coxiella burnetii , also known as the causal agent of Q fever, is a zoonotic pathogen infecting humans and several animal species. Here, we investigated the epidemiological context of C. burnetii from an area in the Hérault department in southern France, using the One Health paradigm. In total, 13 human cases of Q fever were diagnosed over the last three years in an area comprising four villages. Serological and molecular investigations conducted on the representative animal population, as well as wind data, indicated that some of the recent cases are likely to have originated from a sheepfold, which revealed bacterial contamination and a seroprevalence of 47.6%. However, the clear-cut origin of human cases cannot be ruled out in the absence of molecular data from the patients. Multi-spacer typing based on dual barcoding nanopore sequencing highlighted the occurrence of a new genotype of C. burnetii . In addition, the environmental contamination appeared to be widespread across a perimeter of 6 km due to local wind activity, according to the seroprevalence detected in dogs (12.6%) and horses (8.49%) in the surrounding populations. These findings were helpful in describing the extent of the exposed area and thus supporting the use of dogs and horses as valuable sentinel indicators for monitoring Q fever. The present data clearly highlighted that the epidemiological surveillance of Q fever should be reinforced and improved.

Monitoring of tickborne diseases is critical for prevention and management. We analyzed 418 ticks removed from 359 patients during 2014-2021 in Marseille, France, for identification and bacteria detection. Using morphology, molecular methods, or matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, we identified 197 (47%) Ixodes, 136 (33%) Dermacentor, 67 (16%) Rhipicephalus, 8 (2%) Hyalomma, 6 (1%) Amblyomma, 2 (0.5%) Argas, and 2 (0.5%) Haemaphysalis tick species. We also detected bacterial DNA in 241 (58%) ticks. The most frequent bacterial pathogens were Rickettsia raoultii (17%) and R. slovaca (13%) in Dermacentor ticks, Borrelia spp. (9%) in Ixodes ticks, and R. massiliae (16%) in Rhipicephalus ticks. Among patients who were bitten, 107 had symptoms, and tickborne diseases were diagnosed in 26, including scalp eschar and neck lymphadenopathy after tick bite and Lyme borrelioses. Rapid tick and bacteria identification using a combination of methods can substantially contribute to clinical diagnosis, treatment, and surveillance of tickborne diseases.

The emergence of the Coronavirus Disease 2019 (COVID-19) pandemic has fostered the use of high-throughput techniques to sequence the entire severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome and track its evolution. The present study proposes a rapid and relatively less expensive sequencing protocol for 384 samples by adapting the use of an Illumina NovaSeq library to an Illumina MiSeq flow cell instrument. The SARS-CoV-2 genome sequences obtained with Illumina NovaSeq and those obtained using MiSeq instruments were compared with the objective to validate the new, modified protocol. A total of 356 (94.6%) samples yielded interpretable sequences using the modified Illumina COVIDSeq protocol, with an average coverage of 91.6%. By comparison, 357 (94.9%) samples yielded interpretable sequences with the standard COVIDSeq protocol, with an average coverage of 95.6%. Our modified COVIDSeq protocol could save 14,155 euros per run and yield results from 384 samples in 53.5 h, compared to four times 55.5 h with the standard Illumina MiSeq protocol. The modified COVIDSeq protocol thus provides high quality results comparable to those obtained with the standard COVIDSeq protocol, four times faster, while saving money.

Introduction: Cat scratch disease (CSD) is the most common cause of bacterial infectious lymphadenopathy, especially in children, but its diagnosis still remains challenging. Serological assays are widely applied due to their simplicity and the non-invasive sampling. However, these techniques present several limitations, including not well-defined antigen preparation, assay conditions and cutoff titers, severe cross-reactions with other species and organisms, and the notably ranging seroprevalence in the normal population. The objective of this study is to review the literature in order to determine the best diagnostic procedure for the diagnosis of CSD., Methods: Databases including PubMed, Medline, Google Scholar, and Google were searched to determine the best diagnostic procedure for the diagnosis of CSD. A total of 437 papers were identified and screened, and after exclusion of papers that did not fulfill the including criteria, 63 papers were used., Results: It was revealed that sensitivities of serological assays varied from 10% to 100%. Indeed, more than half of the studies reported a sensitivity lower than 70%, while 71% of them had a sensitivity lower than 80%. Moreover, specificities of serological assays ranged from 15% to 100%, with 25 assays reporting a specificity lower than 90%., Conclusion: It is considered that molecular assays should be the gold standard technique for CSD confirmation, and physicians are reinforced to proceed to lymph node biopsy in suspicious CSD cases., Competing Interests: The authors declare that they have no conflicts of interest., (Copyright © 2023 Myrto Koutantou et al.)

The objective of this study was to evaluate the effectiveness of the recommended treatment for endovascular infections due to Coxiella burnetii. This single-center retrospective study was conducted in 13 patients with endovascular infection due to C. burnetii between January 2001 and December 2020 for a definite or possible endovascular infection due to C. burnetii with a minimum follow-up of 18 months post-infection. Clinical and biological data, including serology, blood and tissue PCR results, doxycycline and hydroxychloroquine assays were collected. Among the 13 patients, 11 had endocarditis (8 definite and 3 possible) and 2 had a vascular infection. At the time of diagnosis, fever was present in only 46% of cases. In case of endocarditis, 73% of patients had a pathological echocardiography. Biologically, the CRP level was low (52 mg/l ± 44). Autoimmune antibodies (antinuclear factor, neutrophil anticytoplasm) were present in 23% of patients. At the time of diagnosis, tissue PCR was very sensitive (100%) unlike blood or serum (29%). Blood levels of doxycycline and hydroxychloroquine were within expected values. Only one patient experienced treatment failure at two years, requiring surgery. For the 7 patients whose phase I IgG titres fell below 1/800, a minimum of 18 months of treatment was necessary. In the long term, the clinical and biological cure was 100% and 92% respectively, underlining the importance of monitoring the serum dosages of doxycycline and hydroxychloroquine. Given its sensitivity, tissue PCR could be added to the major Duke criteria., (Copyright © 2022 Japanese Society of Chemotherapy and The Japanese Association for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.)

Judicial Opinion 128 addresses nomenclatural issues related to the names of classes validly published under the International Code of Nomenclature of Prokaryotes. It is confirmed that the common ending -proteobacteria of some class names is not indicative of a joint taxonomic or phylogenetic placement; that the nomenclatural type of Mollicutes Edward and Freundt 1967 (Approved Lists 1980) is Mycoplasmatales Freundt 1955 (Approved Lists 1980); and that the placement of a name on the list of rejected names does not imply that another name with the same spelling but a distinct rank is also placed on that list. The names at the rank of class Anoxyphotobacteria (Gibbons and Murray 1978) Murray 1988, Archaeobacteria Murray 1988, Bacteria Haeckel 1894 (Approved Lists 1980), Firmibacteria Murray 1988, Microtatobiotes Philip 1956 (Approved Lists 1980), Oxyphotobacteria (ex Gibbons and Murray 1978) Murray 1988, Photobacteria Gibbons and Murray 1978 (Approved Lists 1980), Proteobacteria Stackebrandt et al . 1988, Schizomycetes Nägeli 1857 (Approved Lists 1980), Scotobacteria Gibbons and Murray 1978 (Approved Lists 1980) are placed on the list of rejected names. For three common nominative singular suffixes of genus names their genitive singular and nominative plural forms are confirmed: -bacter ( -bacteris , -bacteres ); -fex ( -ficis , -fices ); and -genes ( -genis , -genes ). The class names Aquificae Reysenbach 2002, Chrysiogenetes Garrity and Holt 2002, Chthonomonadetes Lee et al . 2011, Gemmatimonadetes Zhang et al . 2003, Opitutae Choo et al . 2007 and Verrucomicrobiae Hedlund et al . 1998 are orthographically corrected to Aquificia , Chrysiogenia , Chthonomonadia , Gemmatimonadia , Opitutia and Verrucomicrobiia , respectively.

In this paper the Judicial Commission provides general guidance for interpreting the International Code of Nomenclature of Prokaryotes (ICNP) and specific assistance to authors, reviewers and editors of a Request for an Opinion, or of other suggestions related to the ICNP. The role of the Judicial Commission is recapitulated, particularly with respect to the processing of such Requests. Selected kinds of nomenclature-related proposals are discussed that are unsuitable as the basis for a Request. Particular emphasis is put on Requests for placing names or epithets on the list of nomina rejicienda , and a dichotomous identification key is provided to guide potential authors of a Request that targets the name of a species or subspecies because of issues with its type strain. To this end, the criteria for the valid publication of such names under the ICNP are revisited. Aspects of other kinds of Requests are also addressed. The study is based on a comprehensive review of all Judicial Opinions issued since the publication of the Approved Lists in 1980. One goal of this paper is to assist potential authors in deciding whether their concern should be the subject of a Request, and if so, in composing it with the greatest chance of success. It is also clarified how to obtain additional help regarding nomenclature-related issues.

Brucella intermedia (formerly Ochrobactrum intermedium ), a non-fermentative bacterium, has been isolated from animals and human clinical specimens. It is naturally resistant to polymyxins, including colistin (CO), and may cause opportunistic infections in humans. We isolated six Brucella intermedia strains from Senegalese monkey stool. In order to determine whether an efflux pump mechanism was involved in CO resistance in B. intermedia, we evaluated the effects of verapamil (VRP), reserpine (RSP), phe-arg β-naphthylamide dihydrochloride (PAβN) and carbonyl cyanide 3-chloro phenyl hydrazone (CCCP), four efflux pump inhibitors, on these colistin-resistant strains. Using the broth microdilution method, a CO and CCCP combination of 2 µg/mL and 10 µg/mL, respectively, significantly reduced the CO minimal inhibitory concentration (MIC) of B. intermedia , supporting an efflux pump mechanism. In contrast, VRP, PAβN and RSP did not restore CO susceptibility. A time kill assay showed a bactericidal effect of the CO-CCCP combination. Genomic analysis revealed a potential implication in the CO resistance mechanism of some conserved efflux pumps, such as YejABEF, NorM and EmrAB, as previously reported in other bacteria. An inhibitory effect of the CO-CCCP combination was observed on biofilm formation using the crystal violet method. These results suggest that the intrinsic CO resistance in Brucella intermedia is linked to an efflux pump mechanism and that the synergistic effect of CO-CCCP may open a new field to identify new treatments to restore antibiotic efficacy in humans.

The nature and dynamics of mutations associated with the emergence, spread, and vanishing of SARS-CoV-2 variants causing successive waves are complex. We determined the kinetics of the most common French variant ("Marseille-4") for 10 months since its onset in July 2020. Here, we analyzed and classified into subvariants and lineages 7453 genomes obtained by next-generation sequencing. We identified two subvariants, Marseille-4A, which contains 22 different lineages of at least 50 genomes, and Marseille-4B. Their average lifetime was 4.1 ± 1.4 months, during which 4.1 ± 2.6 mutations accumulated. Growth rate was 0.079 ± 0.045, varying from 0.010 to 0.173. Most of the lineages exhibited a bell-shaped distribution. Several beneficial mutations at unpredicted sites initiated a new outbreak, while the accumulation of other mutations resulted in more viral heterogenicity, increased diversity and vanishing of the lineages. Marseille-4B emerged when the other Marseille-4 lineages vanished. Its ORF8 gene was knocked out by a stop codon, as reported in SARS-CoV-2 of mink and in the Alpha variant. This subvariant was associated with increased hospitalization and death rates, suggesting that ORF8 is a nonvirulence gene. We speculate that the observed heterogenicity of a lineage may predict the end of the outbreak., (© 2022 The Authors. Journal of Medical Virology published by Wiley Periodicals LLC.)